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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

ABSTRACT: Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure was assessed in two recent blind tests of protein-structure prediction. During the first blind test, we predicted large fragments of alpha and alpha+beta proteins [60-70 residues with C(alpha) rms deviation (rmsd) <6 A]. However, for alpha+beta proteins, significant topological errors occurred despite low rmsd values. In the second exercise, we predicted whole structures of five proteins (two alpha and three alpha+beta, with sizes of 53-235 residues) with remarkably good accuracy. In particular, for the genomic target TM0487 (a 102-residue alpha+beta protein from Thermotoga maritima), we predicted the complete, topologically correct structure with 7.3-A C(alpha) rmsd. So far this protein is the largest alpha+beta protein predicted based solely on the amino acid sequence and a physics-based potential-energy function and search procedure. For target T0198, a phosphate transport system regulator PhoU from T. maritima (a 235-residue mainly alpha-helical protein), we predicted the topology of the whole six-helix bundle correctly within 8 A rmsd, except the 32 C-terminal residues, most of which form a beta-hairpin. These and other examples described in this work demonstrate significant progress in physics-based protein-structure prediction.

SUBMITTER: Oldziej S

PROVIDER: S-EPMC1140449 | biostudies-literature | 2005 May

REPOSITORIES: biostudies-literature

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Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

Ołdziej S S Czaplewski C C Liwo A A Chinchio M M Nanias M M Vila J A JA Khalili M M Arnautova Y A YA Jagielska A A Makowski M M Schafroth H D HD Kaźmierkiewicz R R Ripoll D R DR Pillardy J J Saunders J A JA Kang Y K YK Gibson K D KD Scheraga H A HA

Proceedings of the National Academy of Sciences of the United States of America 20050513 21

Recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. The conformational space is searched extensively at the united-residue level by using our physics-based UNRES energy function and the conformational space annealing method of global optimization. The lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ECEPP/3 force field. The procedure ...[more]

PMID: 15894609

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Project description:The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in which each amino-acid residue is reduced to two interaction sites, namely, a united peptide group (p) located halfway between the two neighboring ?-carbon atoms (C?s), which serve only as geometrical points, and a united side chain (SC) attached to the respective C?. Owing to this simplification, millisecond molecular dynamics simulations of large systems can be performed. While UNRES predicts overall folds well, it reproduces the details of local chain conformation with lower accuracy. Recently, we implemented new knowledge-based torsional potentials (Krupa et al. J. Chem. Theory Comput. 2013, 9, 4620–4632) that depend on the virtual-bond dihedral angles involving side chains: C?···C?···C?···SC (?(1)), SC···C?···C?···C? (?(2)), and SC···C?···C?···SC (?(3)) in the UNRES force field. These potentials resulted in significant improvement of the simulated structures, especially in the loop regions. In this work, we introduce the physics-based counterparts of these potentials, which we derived from the all-atom energy surfaces of terminally blocked amino-acid residues by Boltzmann integration over the angles ?(1) and ?(2) for rotation about the C?···C? virtual-bond angles and over the side-chain angles ?. The energy surfaces were, in turn, calculated by using the semiempirical AM1 method of molecular quantum mechanics. Entropy contribution was evaluated with use of the harmonic approximation from Hessian matrices. One-dimensional Fourier series in the respective virtual-bond-dihedral angles were fitted to the calculated potentials, and these expressions have been implemented in the UNRES force field. Basic calibration of the UNRES force field with the new potentials was carried out with eight training proteins, by selecting the optimal weight of the new energy terms and reducing the weight of the regular torsional terms. The force field was subsequently benchmarked with a set of 22 proteins not used in the calibration. The new potentials result in a decrease of the root-mean-square deviation of the average conformation from the respective experimental structure by 0.86 Å on average; however, improvement of up to 5 Å was observed for some proteins.

Project description:Three algorithms, namely a Replica Exchange method (REM), a Replica Exchange Multicanonical method (REMUCA), and Replica Exchange Multicanonical with Replica Exchange (REMUCAREM), were implemented with the coarse-grained united-residue force field (UNRES) in both Monte Carlo and Molecular Dynamics versions. The MD algorithms use the constant-temperature Berendsen thermostat, with the velocity Verlet algorithm and variable time step. The algorithms were applied to one peptide (20 residues of Alanine with free ends; ala(20)) and two small proteins, namely an ?-helical protein of 46 residues (the B-domain of the staphylococal protein A; 1BDD), and an ?+?-protein of 48 residues (the E. Coli Mltd Lysm Domain; 1E0G). Calculated thermodynamic averages, such as canonical average energy and heat capacity, are in good agreement among all simulations for poly-L-alanine, showing that the algorithms were implemented correctly, and that all three algorithms are equally effective for small systems. For protein A, all algorithms performed reasonably well, although some variability in the calculated results was observed whereas, for a more complicated ?+?-protein (1E0G), only Replica Exchange was capable of producing reliable statistics for calculating thermodynamic quantities. Finally, from the Replica Exchange molecular dynamics results, we calculated free energy maps as functions of RMSD and radius of gyration for different temperatures. The free energy calculations show correct folding behavior for poly-L-alanine and protein A while, for 1E0G, the native structure had the lowest free energy only at very low temperatures. Hence, the entropy contribution for 1E0G is larger than that for protein A at the same temperature. A larger contribution from entropy means that there are more accessible conformations at a given temperature, making it more difficult to obtain an efficient coverage of conformational space to obtain reliable thermodynamic properties. At the same temperature, ala(20) has the smallest entropy contribution, followed by protein A, and then by 1E0G.

Dataset Information

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

Publications

Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests.

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